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Background: Annual total Gross Primary Production (GPP) and Net Primary Production (NPP) and the annual total stored GPP and NPP are tightly coupled to land cover distributions because the distinct vegetation conditions of different land cover classes strongly affect GPP and NPP. Spatial and statistical analysis tools using Geographic Information Systems (GIS) were used to investigate the spatial distribution of each land cover class and the GPP and NPP based on the CORINE land cover classification in the federal state, Schleswig-Holstein, Germany for the years 2000, 2006 and 2012.Results: "Non-irrigated arable land" and "pastures" were the dominant land cover classes. Because of their large area, "non-irrigated arable land" and "pastures" had higher annual total stored GPP and NPP values than the other land cover classes. Annual total GPP and NPP hotspots were concentrated in the central-western part of Schleswig-Holstein. Cold spots were mainly located in the western and eastern Schleswig-Holstein. The distributions of the annual total GPP and NPP hotspots and cold spots were primarily determined by land cover and land cover changes among the investigated years. The average annual total NPP/GPP ratios were 0.5647, 0.5350 and 0.5573 in the years 2000, 2006 and 2012, respectively. The calculated respiration in 2006 was the highest, followed by those in 2012 and 2000. Conclusions:The land cover classes with high-ability of carbon stocks in 2000, 2006 and 2012 in Schleswig-Holstein were identified in this study. Furthermore, it is recommendable to enhance the annual total GPP and NPP and the annual total stored GPP and NPP in Schleswig-Holstein by replacing the land cover classes showing low carbon stock capabilities with the classes showing high abilities for the purpose of increasing greenhouse gas fixation.